Abstract: Groundwater is a critical component of water resources that supports ecosystem functioning and sustains human water demand. However, the pathways and mechanisms through which changes in groundwater quality affect ecosystems differ fundamentally from those associated with human health. Existing groundwater quality assessment standards, including the commonly adopted Groundwater Quality Standard (GB/T 14848–2017), are primarily designed for drinking-water safety and groundwater quality protection and may not adequately reflect ecological sensitivity in conservation areas. To develop an assessment approach more suitable for ecological protection regions, this study selected the Hongyuan-Ruo’ergai Ecological Reserve region in Sichuan Province, w a region where groundwater quality is predominantly controlled by natural processes, as a case study. Four evaluation approaches, including Worst-Indicator Evaluation, Entropy-Weighted Water Quality Index (EWQI), Water Index (WI), and Classification-Combination Evaluation, were applied and comparatively analyzed. The results indicate that the primary components exceeding standards in the groundwater of the Hongyuan-Ruo’ergai Ecological Reserve are manganese (33.33%), oxygen consumption (21.79%), total hardness (14.10%), and ammonia nitrogen (10.26%). The evaluation results from the four methods varied significantly. The Worst-Indicator method suggests poor water quality in the study area (Class IV and V groundwater accounted for 72.29%), which does not align with the area's minimal human activity. In contrast, WI and EWQI results are markedly different, with more concentrated grade distributions; EWQI is highly sensitive to trace constituents with low absolute content and high variation coefficients, while WI does not explicitly account for transitions across water quality classification boundaries. The Classification-Combination Evaluation shows that the study area is mainly comprised of Class II and III groundwater (accounting for 66.67%), and the evaluation results follow a normal distribution, better reflecting the actual condition of the area. The Classification-Combination Evaluation method takes into account the continuity of indicator concentrations and separately evaluates ecosystem-sensitive indices, toxicological indices, and general chemical indices, providing a flexible and transferable approach for groundwater quality assessment in ecologically sensitive regions.